You wrote:---------
> Darwin did not reject divine creation. He did reject the separate
> creation of most organisms (though allowing for the possibility of
> multiple origins), and he seems to have rejected divine involvement in
> many day-to-day events, to the best of my knowledge, but the latter
> does not follow from the former.
---------------------

No, Darwin most definitely did reject divine creation. He used both implicit
and explicit rejections of creation as his strong arguments. Following pages
and pages of meandering thought experiments, and gee/ maybe/ would-a/
could-a/ 's, he would then make his powerful conclusions about how evolution
must be true because divine creation was obviously failing. Here are two
quick examples:

**************
"What can be more curious than that the hand of a man, formed for grasping,
that of a mole for digging, the leg of the horse, the paddle of the
porpoise, and the wing of the bat, should all be constructed on the same
pattern …"

"How inexplicable are the cases of serial homologies on the ordinary view of
creation!"

***************

You might see my book *Darwin's God* for more details of the role these
arguments played, and many more examples, both from Darwin and later
evolutionsts. Gould summed it up well:

***********

"Odd arrangements and funny solutions are the proof of evolution—paths that
a sensible God would never tread but that a natural process, constrained by
history, follows perforce. No one understood this better than Darwin. Ernst
Mayr has shown how Darwin, in defending evolution, consistently turned to
organic parts and geographic distributions that make the least sense."

**********

God must be "sensible," right?

You wrote:---------
>>CH: "God wouldn't create a Linnean pattern" (characterization of an
> argument for evolution).
>
> This falsely assumes “either God or evolution”. Since Linnaeus assumed
> that the pattern was created, it seems unlikely that many people
> believed such an argument. However, the Linnaean hierarcy in fact
> turns out to match very well with the expected results of evolution.
> On the contrary, it is not clear why separate creation should produce
> such a pattern. Separate creation could produce such a pattern, or any
> other pattern, but why it would produce one in line with the
> expectations of evolution is not evident to me.
---------------------

People have not only believed such an argument, it has been an important
proof text for evolution.

Darwin wrote: "The several subordinate groups in any class cannot be ranked
in a single file, but seem clus-tered round points, and these round other
points, and so on in almost endless cycles. If species had been
independently created, no explanation would have been possible of this kind
of classification." More recent evolutionists agree wholeheartedly:

"If species are separately created there is no reason why they should be
created in large groups of fundamentally similar structure." -- George
Carter

"Could the single artisan, who has no one but himself from whom to steal
designs, possibly be the explanation for why the Creator fashioned life in a
hierarchical fashion—why, for exam-ple, reptiles, amphibians, mammals, and
birds all share the same limb structure?" -- Niles Eldredge

By the way, the Linnean pattern is not, as you say, "line with the
expectations of evolution." It could easily explain other patterns.

You wrote:---------
> it’s worth remembering that rodents and primates
> are rather closely related. Close genetic similarity between humans
> and mice is less surprising than equal human-armadillo similarity would
> be, for example. ... Common descent predicts sequence similarity. Common
> descent does
> not say anything about the conservation of functionally unconstrained
> sequences.
---------------------

The human-mouse-rat UCEs are statistically off the charts. You might want to
read up on them. As for common descent, why does it predict sequence
similarity? Answer: it appeals to evolutionary ideas about speciation. New
species derive from older species via a naturalistic process, such as
mutations. There are no saltations; no miracles. And the mutation rates need
to be in the same ballpark as our empirical observations (though this is
routinely violated by evolutionists). This is all because there is a
on-going, naturalistic, process of *variation* (such as caused by
mutations), that entails no teleology -- no final causes. Hence, mutations
ought to occur randomly in the genome, more or less (another failed
prediction by the way), and in non functional segments they should
accumulate. There is simply no question that common descent predicts that
functionally unconstrained sequences should not be conserved relative to
functional sequences.

You wrote:---------
> You don’t have everything that was in the genome of either of your
> parents. As the provirus is not important for the survival of
> primates, there’s nothing far fetched about its being lost.
---------------------

You wrote:---------
> The use of different genes and
> pathways can readily occur through evolutionary change. Your argument
> about conserved regions claimed that things have to change
> evolutionarily; this claims that things can’t change evolutionarily.
---------------------

You are missing the point. The genes and development pathways routinely are
different for homologous structures, but the end product, the *structures"
themselves have not changed. There is no selection pressure at work here.

Glenn:

GRM: Jonathan Wells seems to disagree with your assertion
"From a design perspective, however, it is possible to regard
develoment as an end-directed process. If organisms are designed,
which is to say produced according to a preconceived plan, then in
some sense their final form precedes their embryonic development.
Rather than rolling freely down the hill, the developmental ball is
attracted to its final resting place, which it could conceivably reach
by a variety of routes unless it is prevented from doing so by
obstacles along the way. Such thinking is anathema to neo-Darwinism,
but before Darwin it was commonplace for embryologists to regard
development as an end-directed process." Jonathan Wells, "Recent
Insights from Developmental Biology," in William A. Dembski, ed., Mere
Creation, (Downer's Grove, Ill.: Intervarsity Press, 1998), p. 51-70,
p.61-62

CH: Wells is talking about the long history of embryology, and all the
metaphysical baggage it has been saddled with. He is countering the
evolution view with an ID view. He is not providing the details of how the
species arose. You mentioned the Nature of Nature conference papers. I'll
have to look at those, thanks. In any case, the kind of information
theory-based ID that Dembski promotes (trying to detect when and where
design can be inferred as opposed to the workings of natural processes) does
not provide the details of how species arise (this is not to say he and
other don't have their own ideas about it).

GRM: And now you start talking about adaptive change, which IS what drives
speciation, when above you claimed that ID had nothing to do with how
speciation occurs. Once again, you flip flop in a most ad hoc fashion.
Discussing things with you is like trying to nail down jello.

CH: What I said was that small-scale adaptive change is a problem for
evolution and common descent. You seem to read everything as coming from ID.

GRM: Please list these [nested hierarchy] violations. BAld, evidentiaryless
assertions are worthless. YOu seem to think that if you say somethign we
must automatically believe that you know what you are talking about.

CH: Here are some places for you to start. There's much more where these
came from.